Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine

Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found, for example, in such macrolide antibiotics as erthyromycin, azithromycin, and clarithromycin. The efficacies of these macrolide antibiotics are markedly reduced in the absence of desosamine. In the bacterium Streptomyces venezuelae, six enzymes are required for the production of dTDP-desosamine. The focus of this X-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose, to a nominal resolution of 2.1 A. Each subunit of the dimeric enzyme contains 12 alpha-helices and 14 beta-strands. Three cis-peptides are observed in each subunit, Phe 330, Pro 332, and Pro 339. The two active sites of the enzyme are located in clefts at the subunit/subunit interface. Electron density corresponding to the bound product clearly demonstrates a covalent bond between the amino group of the product and C-4' of the PLP cofactor. Interestingly, there are no hydrogen-bonding interactions between the protein and the dideoxyglucosyl group of the product (within 3.2 A). The only other sugar-modifying aminotransferase whose structure is known in the presence of product is PseC from Helicobacter pylori. This enzyme, as opposed to DesI, catalyzes amino transfer to the axial position of the sugar. A superposition of the two active sites for these proteins reveals that the major differences in ligand binding occur in the orientations of the deoxyglucosyl and phosphoryl groups. Indeed, the nearly 180 degrees difference in hexose orientation explains the equatorial versus axial amino transfer exhibited by DesI and PseC, respectively.     

Number, unit, and utility in a Mayan community: the relation between use-value, labour-power, and personhood

Rather than asking how two use-values can have the same exchange-value, this article asks how two distinct entities can have the same use-value. Among the Q'eqchi'-Maya, substitution ( eeqaj ) refers to activities as disparate as house-building, civil-religious elections, vengeance, loans, illness cures, adultery, and namesakes. Such practices involve the exchange of one entity for another entity, insofar as these entities have shared properties, and insofar as they hold a role in a necessary position. Substitution is interpreted as social processes whereby substances get utilized, unitized, and numericalized, and this local articulation of use-value is theorized in terms of labour-power and personhood.     

Comparison of the reactivity of B-DNA and Z-DNA with two isosteric chemical carcinogens: 2-N,N-acetoxyacetylaminofluorene and 3-N,N-acetoxyacetylamino-4,6-dimethyldipyrido-[1,2-a:3'',2'' -d] imidazole.

The reactivity of nucleic acids in various conformations and two isosteric chemical carcinogens 2-N,N-acetoxyacetylaminofluorene (N-AcO-AAF) and 3-N,N-acetoxyacetylamino-4,6-dimethyldipyrido [1,2-a:3',2'-d] imidazole (N-AcO-AGlu-P-3) have been studied. Both carcinogens bind covalently to poly(dG-dC).poly(dG-dC) (B form) and to poly(dG-br5C).poly(dG-br5dC) (Z form). They also bind covalently to (dC-dG)16 and to (dG-dT)15 sequences inserted in plasmids when the inserts are in the B form but they do not bind to the inserts in the Z form. The reactivity of guanine residues at the B-Z junctions depends upon the superhelical density of the plasmids and upon the base sequences at the junction. The distribution of AGlu-P-3 modified guanines in a restriction fragment of pBR322 is not uniform and is different from that of AAF-modified guanines. The conclusion is that N-AcO-Glu-P-3 as N-AcO-AAF can probe at the nucleotide level the polymorphism of DNA. On the other hand, the non-reactivity of both chemical carcinogens and Z-DNA and the hyperreactivity of some junctions might have some importance in the understanding of chemical carcinogenesis.     

Synthesis and antimicrobial activity of the symmetric dimeric form of Temporin A based on 3-N,N-di(3-aminopropyl)amino propanoic acid as the branching unit.

Dimeric derivative of antimicrobial peptide amide Temporin A (TA) was synthesized by using a new branching unit 3-N,N-di(3-aminopropyl)amino propanoic acid (DAPPA), which allows building of the parallelly symmetric alpha-helical structures. Antimicrobial effect of the original peptide amide, its monomeric carboxy (TAc) and novel dimeric (TAd) analogues were tested against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative). Both TA and TAd completely inhibited the growth of S. aureus at the concentrations of 5 and 10 microM, respectively, whereas TAc did not show any inhibitory activity. The activities of TAc, TA and TAd correlate directly with the net charges of the molecules, +1, +2 and +4, respectively. Interestingly, TAd displayed antibacterial effect against E. coli at a concentration of 10 microM, where as monomeric TA did not show any activity at concentration as high as 20 microM. The results indicate that the novel structural modification improves the antibacterial properties of Temporin A especially towards Gram-negative bacteria.     

New fluorescent bile acids: synthesis, chemical characterization, and disastereoselective uptake by Caco-2 cells of 3-deoxy 3-NBD-amino deoxycholic and ursodeoxycholic acid

Deoxycholic acid (DCA), a secondary bile acid (BA), and ursodeoxycholic acid (UDCA), a tertiary BA, cause opposing effects in vivo and in cell suspensions. Fluorescent analogues of DCA and UDCA could help investigate important questions about their cellular interactions and distribution. We have prepared a set of isomeric 3α- and 3β-amino analogues of UDCA and DCA and derivatised these with the discrete fluorophore, 4-nitrobenzo-2-oxa-1,3-diazol (NBD), forming the corresponding four fluorescent adducts. These absorb in the range 465-470 nm and fluoresce at approx. 535 nm. In order to determine the ability of the new fluorescent bile acids to mimic the parents, their uptake was studied using monolayers of Caco-2 cells, which are known to express multiple proteins of the organic anion-transporting peptide (OATP) subfamily of transporters. Cellular uptake was monitored over time at 4 and 37°C to distinguish between passive and active transport. All four BA analogues were taken up but in a strikingly stereo- and structure-specific manner, suggesting highly discriminatory interactions with transporter protein(s). The α-analogues of DCA and to a lesser extent UDCA were actively transported, whereas the β-analogues were not. The active transport process was saturable, with Michaelis-Menten constants for 3α-NBD DCA (5) being K(m)=42.27±12.98 μM and V(max)=2.8 ± 0.4 nmol/(mg protein*min) and for 3α-NBD UDCA (3) K(m)=28.20 ± 7.45 μM and V(max)=1.8 ± 0.2 nmol/(mg protein*min). These fluorescent bile acids are promising agents for investigating questions of bile acid biology and for detection of bile acids and related organic anion transport processes.     

Synthetic receptor analogues: preparation and calculated conformations of the 2-deoxy, 6-O-methyl, 6-deoxy, and 6-deoxy-6-fluoro derivatives of methyl 4-O-alpha-D-galactopyranosyl-beta-D-galactopyranoside (methyl beta-D-galabioside)

The 2-deoxy (7), 6-O-methyl (15), 6-deoxy (22), and 6-deoxy-6-fluoro (31) derivatives of methyl beta-D-galabioside (1) have been synthesised. Thus, 7 was prepared by xanthate reduction using tributyltin hydride, whereas 22 was obtained by catalytic hydrogenation of a 6-deoxy-6-iodogalabioside. Regioselective monofluorination of methyl 2,3-di-O-benzoyl-beta-D-galactopyranoside with Et2NSF3 and subsequent alpha-D-galactosylation provided 31. Molecular mechanics calculations yielded similar conformations for 1, 7, 15, 22, and 31 with differences in phi H and psi H of less than 5 degrees. No indications of intramolecular hydrogen bonds, as displayed by 1 in the crystal, were found for 7, 15, 22, or 31.     

Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins

Structural distributions of each amino acid were compared between 20 pairs of thermophilic and mesophilic proteins to obtain thermostable factors. Five kinds of residual structure states such as fully-exposed, exposed, partially exposed (or partially buried), buried, well-buried states were considered for analyzing the structural patterns of amino acids. The statistical tests revealed that lower frequency in partially exposed state of SER, lower frequency in exposed state and higher frequency in well-buried state of ALA, higher frequency in buried state of GLU, higher frequency in exposed state of ARG, etc. could be critical factors related with protein thermostability.     

Protein thermostability: structure-based difference of residual properties between thermophilic and mesophilic proteins

Structure-based differences of residual properties between 20 pairs of thermophilic and mesophilic proteins were statistically analyzed to elucidate the factors governing protein thermostability. This study analyzed the distributions of outer residues, inner residues, flexible residues, rigid residues, hydrogen bonds, salt bridges, cation–pi interactions, and disulfide bonds in each protein in terms of residual structural states, which were determined as five kinds of states under residual packing value. Their structural patterns found in thermophilic protein groups were compared with those of mesophilic protein groups for showing distinctive difference of residual properties. The results of statistical tests (t-test) revealed that flexible residues in fully-exposed state and boundary state, salt bridges in exposed state, and hydrogen bonds in well-buried state could be critical factors related with protein thermostability. Such structure-based differences of residual properties would help to develop a strategy for enhancing protein thermostability.     

Study of the interaction between a histidine-deoxyguanosine hybrid and cisplatin

 A histidine-2′-deoxyguanosine hybrid, Phac-Hse(p^5′dG)-His-OH (I), was synthesized, and its reaction with cisplatin was monitored by reversed-phase HPLC and ¹H NMR. Two new compounds, II and III, were observed to be simultaneously formed, II in larger proportion than III. These products were isolated after HPLC purification and extensively characterized. Both II and III contained platinum, had the same mass and showed a bathochromic displacement of their absorption maxima with respect to that of I. Both remained undegraded upon enzymatic digestion and yielded I when treated with NaCN. From these data and the information provided by ¹H NMR analysis, we inferred that II and III were constitutional isomers, in particular chelates in which platinum was coordinated to the N7 of guanine and either the N^π or the N^τ imidazole nitrogens, respectively. No preference of the metal for either of these N-donors was observed. Received: 3 May 1999 / Accepted: 24 August 1999     

19-oxygenations of 3-deoxy androgens, potent competitive inhibitors of estrogen biosynthesis, with human placental aromatase

Aromatase is a cytochrome P450 enzyme complex that catalyzes the conversion of androst-4-ene-3,17-dione (AD) to estrone through three sequential oxygenations of the 19-methyl group. To gain insight into the ability of 3-deoxy derivative of AD, compound 1, and its 5-ene isomer 4, which are potent competitive inhibitors of aromatase, to serve as a substrate, we studied their 19-oxygenation by human placental aromatase and the metabolites isolated were analyzed by gas chromatography–mass spectrometry. Inhibitors 1 and 4 were found to be oxygenated with aromatase to produce the corresponding 19-hydroxy derivatives 2 and 5 and 19-oxo derivatives 3 and 6 as well as the 17β-reduced 19-hydroxy compounds 7 and 8. Kinetic studies indicated that the 5-ene steroid 4 was surprisingly a good substrate for the aromatase-catalyzing 19-oxygenation with the V_max value of 45 pmol/min per mg prot which was approx. four times higher than that of the other. The relative K_m value for steroids 1 and 4 obtained in this study is opposite from the relative K_i value obtained previously in the inhibition study. The results reveal that there is a difference between a binding suitable for serving as an inhibitor of aromatase and a binding suitable for serving as a substrate of the enzyme in the 3-deoxy steroid series and the C-3 carbonyl group of AD is essential for a proper binding as a substrate to the active site of aromatase.     

Papilio nandina, a probable hybrid between Papilio dardanus and Papilio phorcas

Abstract. Hybrids bred in the laboratory between Papilio dardanus Brown and Papilio phorcas Cramer resulted in male butterflies similar to the two naturally occurring males described as P.nandina Rothschild & Jordan. A single female hybrid insect resembling the female parent was also bred. Male hybrids were also obtained between P.dardanus and P.demodocus/demoleus but not between P.dardanus and P.constantinus .
The phylogenetic relationships of dardanus and phorcas are discussed, and reasons given for preferring the older hypothesis that male-like females are primitive rather than that they represent the most specialized forms. Further information on this point would be forthcoming if backcrosses and F₂ s could be obtained.